Reflecting the themes of the book, the structure of the plot is based on order, a disruption of the order, and a reestablishment of a new kind of order. The novel begins as a straightforward whodunit, as Christopher tries to solve the death of Wellington. A second mystery is also in the process of being solved, which he initially does not realize. When he does, the seemingly simple problem of a dog's death takes on a new dimension. Then, the mystery narrative is disrupted in the middle of the novel: both mysteries, the overt and the covert, are solved by Ed Boone's confession. From there, a less esoteric kind of puzzle-solving (going from point A to point B, Swindon to London) and a more everyday narrative (uniting with his mother and taking his A-level math exam) takes over.
Thus, the mystery of the novel is itself built on a trope that Christopher does not mention: the MacGuffin, which is a Red Herring which starts the action but misdirect readers away from the true central plot. This is how the second, hidden mystery manifests itself, as the details of that hidden mystery - the affair of Judy Boone and Roger Shears, then their running away to London together - becomes entwined to the facts surrounding Wellington's death.
In being a mystery novel of this kind, the book is also a kind of bildungsroman - the solving of the mystery is also a means for education and a new level of self-awareness for Christopher. For him to completely solve the mysteries of who killed Wellington and whether his mother is dead, Christopher not only learns new things about his parents but also forces himself to undergo difficult tasks that he would have otherwise avoided - most notably, taking the train to London.
The mystery plot also allows a family history to emerge, one which eventually takes over the book: in piecing together details about Wellington and the other Shears, Christopher discovers the truth about his mother and father. He also describes what his life was like when he was young and his mother was around. To complete the obvious gap in this family history - what his mother did after leaving Swindon and before returning with Christopher - we have Judy Boone's letters.
Finally, there is a metafictive thread in the narrative - that is, the story calls attention to its being created, as the narrator Christopher discusses how exactly he writes the story that we read. Unlike other books that employ metafictive devices, this self-reflexivity isn't used to subvert or upset traditional narrative conventions - if anything, it's Christopher's unique perspective that upsets those conventions and not the metafictive elements. Rather, the act of writing the book is part of Christopher's claim to being able to do anything he wants - an assertion of control in the very narrative of his life, which he shares with the readers.